The Diversity of NLRs inBrassica rapaPan-genome

Abstract

AbstractThe speciesBrassica rapais mainly cultivated as a vegetable crop with high economic value. But infectious diseases, such as soft rot disease and clubroot disease can cause severe yield losses. Introducing resistance genes through breeding is an efficient and sustainable way to reduce the susceptibility and improve the yield of crops. Nucleotide-Binding Leucine-Rich Repeat (NLR) genes are the main types of resistance genes. They can recognize pathogen effectors and initiate downstream immune response. However, the intraspecific diversity ofNLRgenes inBrassica rapahas remained unknown. Based on domain similarity search and machine learning pipeline, we identified 2188 NLRs in 17 accessions ofBrassica rapagenomes, which constitute the species-wide pan-NLRome inBrassica rapa. The diversity of the four types ofNLRgenes are significantly different in the aspects of chromosome location, number stability, integrated domains (IDs), evolutionary trajectory, and positive selection sites. Phylogenetic analyses show TNL-type NLRs whose N terminus contain Toll/interleukin-1 receptor (TIR) domain experienced accession-specific expansion. Moreover, the expanded TNL-type NLRs carry more positively selected amino acid residues which are mainly located on the protein surface based on their 3D structures. These evidences might imply their important biological function in perceiving pathogen effectors. Taken together, our study provides better insights into the diversity and variation ofNLRgenes inBrassica rapapangemone, which can facilitate the biofunction assigning, cloning, and subsequent application in breeding programs.